I have a heavy mite load, getting ready to use apiguard and read that all honey supers need to be removed prior to this treatment. I have always been told to leave honey for bees to overwinter. Will there be enough time for them to make more or is there enough in my brood boxes to sustain them?
Hi Sheryl and welcome!
The precaution to remove the supers applies just to the ones you will harvest for consumption. Definitely leave adequate stores for the bees.
Good luck getting the mites under control! 
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I might check the amount of honey they have in their brood frames too. Usually there is a bunch of capped honey along the corners. Bees are a little like me in that regard. I don’t want to walk all the way to a storage unit if there’s still space for sweets in a drawer at my desk. 
You can always add the honey super back once you’ve finished the treatment. But - it might depend on where you live - usually you want to remove the honey super for the winter anyway.
Otherwise the bee cluster might move up into the honey super over the winter and since the queen can not follow through the excluder, she will be left behind and die.